8SYC | pdb_00008syc

Crystal structure of PDE3B in complex with GSK4394835A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.224 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Discovery and SAR Study of Boronic Acid-Based Selective PDE3B Inhibitors from a Novel DNA-Encoded Library.

Rowley, A.M.Yao, G.Andrews, L.Bedermann, A.Biddulph, R.Bingham, R.Brady, J.J.Buxton, R.Cecconie, T.Cooper, R.Csakai, A.Gao, E.N.Grenier-Davies, M.C.Lawler, M.Lian, Y.Macina, J.Macphee, C.Marcaurelle, L.Martin, J.McCormick, P.Pindoria, R.Rauch, M.Rocque, W.Shen, Y.Shewchuk, L.M.Squire, M.Stebbeds, W.Tear, W.Wang, X.Ward, P.Xiao, S.

(2024) J Med Chem 67: 2049-2065

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01562
  • Primary Citation of Related Structures:  
    8SYC

  • PubMed Abstract: 

    Human genetic evidence shows that PDE3B is associated with metabolic and dyslipidemia phenotypes. A number of PDE3 family selective inhibitors have been approved by the FDA for various indications; however, given the undesirable proarrhythmic effects in the heart, selectivity for PDE3B inhibition over closely related family members (such as PDE3A; 48% identity) is a critical consideration for development of PDE3B therapeutics. Selectivity for PDE3B over PDE3A may be achieved in a variety of ways, including properties intrinsic to the compound or tissue-selective targeting. The high (>95%) active site homology between PDE3A and B represents a massive obstacle for obtaining selectivity at the active site; however, utilization of libraries with high molecular diversity in high throughput screens may uncover selective chemical matter. Herein, we employed a DNA-encoded library screen to identify PDE3B-selective inhibitors and identified potent and selective boronic acid compounds bound at the active site.


  • Organizational Affiliation

    GSK, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-inhibited 3',5'-cyclic phosphodiesterase 3BA,
B [auth D]
443Homo sapiensMutation(s): 5 
Gene Names: PDE3B
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q13370 (Homo sapiens)
Explore Q13370 
Go to UniProtKB:  Q13370
PHAROS:  Q13370
GTEx:  ENSG00000152270 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13370
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.224 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.586α = 90
b = 78.586β = 90
c = 166.339γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted X5WClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references